BN0651 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 5.5494e-07 3.4919e-03
Layer 4 1.1090e-05 9.7480e-03
Layer 3 1.2153e-05 9.3255e-02
Layer 5 1.8769e-03 1.5562e-02
Layer 1 9.7755e-01 6.8942e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
LY6E Expression Distribution
Gene Specificity Score (GSS)
LY6E GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
LY6E Layer 2 2.3418 0.6508
RAB3A Layer 2 2.2227 0.6418
SYN1 Layer 2 2.1289 0.6383
ENTPD6 Layer 2 2.0820 0.6366
PTOV1 Layer 2 2.1650 0.6360
GOT2 Layer 2 2.3340 0.6340
CLTB Layer 2 2.2422 0.6329
NISCH Layer 2 2.2578 0.6323
SNCA Layer 5 2.3086 0.6310
ARHGDIG Layer 2 1.9629 0.6310
SEC11C Layer 2 2.1445 0.6292
AMPH Layer 2 2.5898 0.6278
GLS Layer 2 2.3086 0.6276
DGCR2 Layer 2 2.1055 0.6268
CALY Layer 2 2.3467 0.6261
CAMKV Layer 2 2.3242 0.6255
CTXN1 Layer 2 2.5869 0.6238
H1FX Layer 2 2.2900 0.6233
BRK1 Layer 2 2.4727 0.6227
STMN4 Layer 2 2.0801 0.6217
SYNGR3 Layer 2 2.1631 0.6187
PTPRN Layer 2 2.1445 0.6171
CLIP3 Layer 2 2.1719 0.6159
CLASP2 Layer 2 2.2148 0.6158
BEX4 Layer 2 2.3057 0.6144
FXYD6 Layer 2 2.4023 0.6140
MADD Layer 2 2.1289 0.6140
POLR2I Layer 2 2.5117 0.6139
TCEAL2 Layer 2 2.1543 0.6139
RPS26 Layer 2 2.5615 0.6134
MLF2 Layer 2 2.2227 0.6130
PNMA8A Layer 2 2.3555 0.6122
ATP9A Layer 2 2.1191 0.6122
NDUFB11 Layer 2 2.2852 0.6116
ATCAY Layer 2 2.1465 0.6114
DYNLRB1 Layer 2 2.1719 0.6112
RACK1 Layer 2 2.1289 0.6111
APBB1 Layer 2 2.0820 0.6110
FKBP8 Layer 4 1.9941 0.6102
ATL1 Layer 2 2.5957 0.6101
ATP6AP1 Layer 2 2.3467 0.6101
ATP6V0E2 Layer 2 2.2969 0.6100
CAMKK1 Layer 2 2.6104 0.6094
CAP2 Layer 2 2.3438 0.6091
RNASEK Layer 2 2.5723 0.6090
CA11 Layer 2 2.1387 0.6090
SH3GL2 Layer 2 2.1562 0.6090
CTSB Layer 2 2.1719 0.6076
AGAP3 Layer 2 2.0938 0.6075
FAM168B Layer 2 2.3242 0.6075

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0651
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0651_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0651/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0651/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0651/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0651/report/PD/BN0651_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0651/report/PD/BN0651_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:00:14
  • Number of Processes: 10
  • Spending Time: 0h 2m